


Submerged in Seclusion

by writerdragonfly



Series: an ever present destiny [3]
Category: Stargate Atlantis
Genre: Additional relationship tags may appear later as well, Alternate Universe - Canon Divergence, Alternate Universe - Sentinels & Guides, Alternate Universe - Sentinels and Guides Are Known, Alternate Universe - Soulmates, M/M, Other Additional Tags to Be Added, Sentient Atlantis, characters will be tagged as they appear
Language: English
Status: In-Progress
Published: 2016-07-24
Updated: 2016-12-01
Packaged: 2018-07-26 08:36:12
Rating: Mature
Warnings: No Archive Warnings Apply
Chapters: 3
Words: 8,138
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/7567438
Author URL: https://archiveofourown.org/users/writerdragonfly/pseuds/writerdragonfly
Summary: <blockquote class="userstuff">
              <p>John Sheppard had grown up believing he would never come online, and his years in the Air Force certainly seemed to prove it. But then he sits in a chair in Antarctica, and something in the pit of his stomach makes a tiny part of himself wonder if he might be wrong. Rodney McKay hadn't even considered the possibility of himself being latent. </p><p>But then they're in the Pegasus Galaxy, in Atlantis, and everything they thought they knew about themselves seems to be changing. Faced with almost certain death, the city itself starts to come alive--through the guardians who protect it.</p><p>Directly follows Prelude to Submersion.</p>
            </blockquote>





	1. Part One

**Author's Note:**

> Hiya, super happy to get this out there. :)
> 
> The first two chapters contain some dialogue from _The Rising_.
> 
> Please enjoy~!

“He's latent,” Dr. Weir argues vehemently, her eyes narrowed in focused threat at the Colonel.

 

“I don't want someone who is _proven_ to disobey orders in my command, Dr. Weir,” Sumner argues back. Weir doesn't stand down, just stiffens her shoulders.

 

“And if we get there and the equipment rejects us since no one has a strong enough gene except perhaps Beckett?”

 

“Then we dial home and--”

 

“And if there isn't enough _power_ to do that?”

 

Sumner keeps her steady gaze for a few long moments before he looks away.

 

“I want it on file that this decision was not one I am comfortable with.”

 

“Noted.”

 

-x-

 

It's addictive, the Chair. It's everything coming online is supposed to feel like according to the Internet. Except, when he's not touching it, everything feels a little hollow.

 

Like he's supposed to be online, supposed to feel that alive, all the time.

 

But he isn't, doesn't.

 

It's almost a relief, then, when they send him back Stateside. No Chair, no temptation. Or so the theory goes.

 

-x-

 

 

When he was ten, David found a penny on the ground. It was heads up, still shiny and clean like it had just been minted. Except it was the same age as John was, and David had given it to him as a gift.

 

John would never admit it, but it was his good luck charm, even now.

 

It hadn't helped him come online nor had it saved his marriage.

 

But he was convinced it saved his life countless times when he was in danger of losing it, even when the drone nearly took down his bird.

 

It only seems fitting to flip it when the decision to stay or go comes down to the wire.

 

Heads, _I finish out my run and find somewhere else to fly._ Tails, _I follow my gut._

 

Heads or tails, stay or go, yes or no.

 

Tails was always his favorite character in Sonic anyway.

 

-x-

 

The months that follow are filled with exhausting paperwork, field tests, weapons placement, Stargate travel.

 

It's not a simple case of See Stargate, Have Address, Will Travel.

 

No matter how much he might wish it was.

 

But it's easy, in his downtime, to wander the labyrinthine halls, peering into windows and open doors.

 

It's easy, perhaps far more easily than he expected, to come to enjoy the late nights when the solitude of being alone gets too much and he sneaks into McKay’s temporary lab in the Mountain.

 

Sometimes they talk, but mostly John listens. Very rarely, John finds himself drawn inexplicably to McKay’s board of equations, where something pulls him in and keeps him occupied until his fingers itch for a pen or a pencil or a marker--anything he can use to spill out the numbers until they _sit_ **_right_** with him.

 

He doesn't do it though, not in front of McKay. Not in front of anyone.

 

It's one thing for a Guide, latent or not, to be attracted to the pull of knowledge. It's different with mundanes, too, to crave that. (And he hates that word--mundanes. As if they're lesser than everyone because they don't share whatever quirk of biology it is that sparks the little extra in Sentinels and in Guides.)

 

John wonders, sometimes, if he's spent too long in the military, too long in worlds that have clear cut rules and regulations, where it's easy to fall back on the stereotypes that are so easily presented because you're supposed to fit into this picture perfect box.

 

But maybe he's just looking for an excuse that would explain why he's so afraid someone will look at him and see something more than an absurdly latent stupid trust fund baby officer.

 

He used to live for this, _math_. Numbers spoke to him in a way that only flying had ever rivaled. They were... _more_... than anything else.

 

He loved the wind in his face at the top of a Ferris Wheel, nothing but sky ahead of him, the world gone. And he loved football, especially college football, the snap of the throw, the cheer of the crowd, the rush of running. 

 

(But going fast, in cars or trains, but especially in planes, was like _living math_. Nothing but speed and equations running through his head.)

 

Even in Ferris Wheels, the math was there. Even in football, watching those impossible passes and knowing, _knowing_ , that the math said the chances of that working, just like that, just in time, were nearly innumerable...

 

Maybe he still lived math, in bullet trajectories and steep dives, equations running through his head like the snap of his fingers, until it was _muscle memory_ instead of that deep, thoughtful wonder that had brought him to Stanford all those years ago.

 

So John wants to work out the math, the math of a man far smarter than him, even without the consideration of the stereotype he presents.

 

But he doesn't.

 

He can't.

 

-x-

 

But he does.

 

He does it, later. Lying in his bunk with the numbers burned into the back of his eyelids. Just one little equation, one little script scrawled in his day planner. Just... one.

 

Somehow instead of the Chair, the deep intoxicating lure of _no longer alone_ , he's become addicted to the pull of numbers again.

 

And addicted to spending time in that lab, sitting with McKay as he rants and raves about the stupidity of his subordinates and superiors alike. He's become addicted to the way it _calms_ him.

 

The math invigorates him. Hell, even McKay’s passionate explanations invigorate him.

 

But there's something about the man himself--and maybe it's because that's what he saw that day, in the chair, that's what he heard, that voice like flying, “ _Major, think about where we are in the solar system._ ”

 

Or maybe the years of emotionally secluded latency have begun driving him insane.

 

Maybe both.

 

-x-

 

McKay was such an asshole, but he was _honestly_ one.

 

-x-

 

Somehow the months between that _moment_ in the Chair for the first time and the breaking dawn of Expedition Day feel like decades and seconds all wrapped into one. Like forever and not enough.

 

John isn't stupid. He knows that though Weir wanted him along (and McKay and Beckett, and probably a great deal more of the science staff), Sumner didn't. It wasn't because of his latency or the fact that he _was_ a Sentinel. John didn't have to have his senses awakened to know that.

 

John had made a choice after a series of choices, that countermanded his commanding officer. It was the _right_ choice, John would never believe otherwise. But it was a dangerous and potentially fatal choice, one that wasn't supposed to be _his_ choice to make--not supposed to be a choice _at all--_ not according to his commander or the board of inquiry that resulted.

 

A history of subverting _any_ orders didn't make for a pretty picture to bring alongside into a potential one-way trip into another _galaxy._ It didn't even make for a pretty picture to take anywhere but Antarctica, where his duty had been nothing but white as far as the eye could see and the silence of his black mark.

 

But he _was_ here, checking his bunk one last time before he joined the rest of the military command that would be heading out into a brave new world. He would be joining them.

 

The Stargate shouldn't flip him online, it hadn't yet. Even with the longer journey, there was nothing to suspect it would effect him at all, if the scientists were to be believed.

 

And he'd known since that first briefing, months ago, with Weir and McKay and Beckett and Jackson and O’Neill... it _could_ be one way. Could be the end of the line, for him.

 

But he'd faced fear head on for years, had seen his end just seconds away and still remained totally and utterly latent. How could this, even drenched with uncertainty, be any different?

 

“Sheppard,” McKay says from the doorway, a sliver in his voice that John instinctively _knew_ was hesitance, even though he'd never once heard it.

 

“McKay,” John replies, and McKay seems to relax, just a _little_ at his name.

 

“What if--”

 

It's reckless and stupid, John knows that light years before he does it. But it doesn't stop him. He's about to walk through a _wormhole_ to another galaxy for what could be the last moments of his life. He's thirty-seven years old, and might never come online, and he wants, even if it's just once, to know what it would be like.

 

So he kisses him, pulling back before Rodney McKay can react _either way_ , and leaves the room.

 

-x-

 

He steps through the Stargate into Atlantis, and it doesn’t feel like Earth but it doesn’t feel like sitting in the Chair had either. He steps forward, somehow keenly aware of McKay gravitating to his side just as surely as he had gravitated to McKay’s all those nights in the Mountain.

 

The steps light up under his feet with a hum, and it reminds him of his first time back in the States after Nancy divorced him, when he’d explored Boston like he was considering leaving the Air Force to go to MIT, alone and _lonely_ , walking up the musical stairs in the Boston Museum of Science, each step a different note.

 

Except, each step feels more like the Chair, and each step seems to enhance his awareness that McKay is beside him and isn’t demanding answers that John doesn’t know how to give, but he’s still _there_.

 

Of course, it doesn’t take long for things to spiral out of control.

 

-x-

 

There’s a taste at the back of his mouth that reminds him of salt water and blood.

 

-x-

 

“Major, I want you to go along,” Weir says, and John nods.

 

“Yes, ma’am.”

 

Except, before he can follow them out toward the Stargate, McKay grabs his arm.

 

“We are going to talk about it, Sheppard,” he says, “Later.”

 

The look on Weir’s face is a mix of confusion and curiosity, but John doesn’t think she’ll ever expect the truth.

 

“Yeah, yeah,” John wants to say, but he catches something indecipherable in McKay’s face that leaves him breathless.

 

“Duty calls,” he manages to get out, and then he’s gone.

 

-x-

 

“It is Halling,” their guide says as he enters the tent ahead of them, “I bring men from away.”

 

The voice inside tells them to enter, and Halling holds open the flap without a second wasted.

 

The woman inside turns to face them, meeting their eyes without fear or hesitance. The torchlight casts shadows about the tent, and only after they step further in does John notice the slight swell of her stomach.

 

“These men wish to trade,” Halling says, stepping to her side. She does not rest an arm on him as John half-expected, but instead tilts her head just slightly to the left.

 

“Ah, it’s nice to meet you,” John manages to say, pasting a smile on his face and pulling her attention toward him.

 

“I am Teyla Emmagan, daughter of Tagan.”

 

"Colonel Marshall Sumner, Major Sheppard, Lieutenant Ford," Sumner introduces, "We have very few specific needs."

 

Emmagan keeps his gaze with an eerie strength and replies without looking away, "We do not trade with strangers."

 

"Is that a fact?"

 

Before the situation worsens, John impulsively starts speaking again, "Well, then, we'll just, uh, have to get to know each other."

 

-x-

 

“The Wraith will come,” Teyla says, and John can hear the capital letters in the word as she does. Wraith.

 

“Who are these Wraith?” Sumner asks before anyone else can, and John can almost feel the temperature of the room grow colder with every passing second.

 

Teyla shares a surprised look with the man at her side, before turning back to them, “We have never met anyone who did not know.”

 

“You have now.”

 

Teyla shakes her head, just slightly, “if the Wraith have never touched your world, you should return there.”

 

Her words sound like a portent, and John is afraid to know what will come.

 

-x-

 

“Your leader looks through me as if I were not there,” Teyla remarks, a hand brushing lightly against her stomach.

 

“Do I?” he asks before he can stop himself.

 

She grins at him, wide and open. “No,” she admits, before her face shutters, “You truly cannot return to your world?”

 

“No.”

 

“Then there is something you must see.”

 

-x-

 

“How far is this place?” John asks, trudging behind her.

 

Teyla pauses, her head tilting just to the side again before she rights herself.

 

“Not far...” she says softly, but she makes no effort to continue walking.

 

“What is it?”

 

“Your leader... is it because of the child or because I am unbonded?”

 

“You’re a Sentinel?”

 

“Sentinel? I do not know that word... My people call me a Keeper. Perhaps it is the same?”

 

-x-

 

"Tell me some good news, Rodney," Elizabeth says, the hint of a smile on her face.

 

Rodney swallows, "I can't do that."

 

"... the shield has held back the ocean for centuries." Elizabeth frowns.

 

"And probably would have kept going for years more, but our arrival changed that. Now it's nothing more than a thin shell between the buildings and the water."

 

"We stopped exploring," she protests.

 

"The damage was already done," Rodney tells her, "Another section of the city on the far side was flooded an hour or so ago."

 

"Even occupying this room is draining power," Grodin adds.

 

He doesn't want to say it, but before it even comes out of his mouth he knows he needs to, "We need to evacuate the moment Colonel Sumner reports back it's safe."

 

"You're saying we have to abandon the city?"

 

He can hear it. Another part of the shield fails and more of the city floods, "the sooner we leave, the longer that shield holds."

 

It doesn't feel _right_.

 

_None of it._

 

He rubs his lucky coin between his fingers, and breathes.


	2. Part Two

**Notes for the Chapter:**

> And now, a look into Rodney's side of things. This chapter is a little longer than the last one, but I don't think ya'll mind that too much. :)
> 
> We definitely start to go the route of canon divergence with this one, fair warning. But I do hope you all enjoy it. 
> 
> I am nervous about this one, so please let me know what you think. <3

“Colonel, this is Sheppard,” the radio squawks, “What you see on the ground is just an illusion. Concentrate on firing on the ships.”

 

Marshall immediately shouts out to his men, “Fire on the ships! Fire on the ships!”

 

He runs to Sergeant Bates, who stands eerily still, his pupils blown wide. But the man doesn't seem to notice him, not even when he shakes him.

 

“Bates, snap out of it! Bates, c’mon!” he yells, once, twice, three times.

 

Bates finally responds, meeting his gaze with his eyes still dilated, “They're everywhere, sir!"

 

Marshall drags him out into the open and points toward the strange ship in the sky, "Take that thing down!"

 

Bates does as requested, makes a near impossible shot when the ship darts forward suddenly. It explodes brightly in the dark of the sky.

 

Except, then another ship comes, and a bright white light engulfs them.

 

-x-

 

Rodney had always been afraid. Fear, in any form, was nothing new.

 

He remembers being a kid, four years old, and knowing that his parents would never understand him. That they weren’t smart enough to do so. Instead of growing up surrounded by love and _any attempt_ at it, he’d been shipped off to a series of teachers and schools where half the time they struggled to understand him too.

 

He was brilliant, always had been. And sometimes, even now, that scared him far more than anything else did.

 

He was eight when Jeannie was born. Eight years old and far ahead of his peers and _so alone_. He didn’t get to spend much time with her until he was nearly thirteen, and his parents called him home without explaining anything.

 

“She’s your responsibility now,” his father had said, pushing Jeannie toward him. He’d looked at his mother, and she looked deliberately away from him.

 

“Merry?” Jeannie had asked, and she was so little and so confused. And then he knew.

 

Even at twelve, he knew it was utterly ridiculous for them to blame _him_ for their second chance being just as smart as he was. “It’s okay, Jeannie. I’ll teach you.”

 

He’d been terrified then. Terrified of doing the wrong thing, saying the wrong thing, screwing up Jeannie’s life as surely as his parents had screwed up his. Terrified that he wouldn’t be able to love her enough to make up for their parents suddenly _not_ loving her.

 

He never really stopped being afraid. He just got really good at pretending he wasn’t always that way.

 

-x-

 

“How are we doing?” Elizabeth asks, “Look, if we can just buy ourselves another day, maybe we could ...”

 

He wondered when it was that he stopped being able to-- _no, **no**. That was ridiculous_.

 

“This city is sacrificing parts of itself in order to maintain these main areas but catastrophic failure is inevitable,” Rodney admitted

 

“Not in my wildest dreams would I hope to find the lost city of the Ancients so completely untouched, so pristine, and we have no choice but to walk away from this?” There's something in her voice that he doesn't like. He doesn't know what it is, perhaps the wistfulness?

 

But Elizabeth’s joy at the idea of Atlantis never bothered him before, so why would it now?

 

“In order to save it,” he retorts, trying to keep his oddly growing uneasiness out of his voice.

 

“To save it for whom?” she asks, as if the idea of anyone else living there is wrong, “We don't have enough power to send a message. As far as Earth is concerned we're just going to be missing, presumed lost.”

 

It wasn’t like that was a lie, but still... something about Elizabeth’s words are steadily making him more and more uncomfortable. “We'll be back,” he manages to say, “We'll find a power source somewhere in Pegasus.”

“We have yet to hear from Colonel Sumner. We've got no idea what's out there.”

 

“We can't wait. It is time to go now.”

 

Muffling a frustrated sigh, Elizabeth walks a few feet away and activates her radio, “Attention all personnel. This is Weir.”

 

The city starts to shake, violent jerky movements that leave them all off-balanced and uneasy.

 

“Stand by for immediate evacuation,” Elizabeth finishes, turning to Rodney, “Dial the Gate.”

 

He presses two chevrons, the buttons lighting up under his fingertips, but then the Gate starts dialing in and pulls control away from him, “We've got an incoming wormhole.”

 

The shield closes quickly, and then the woosh of the Gate activating sounds through the Gateroom.

 

“I'm reading Lieutenant Ford's identification code,” Grodin informs them, his eyes flickering toward Rodney before settling on Elizabeth.

 

 _He feels it too,_ Rodney thinks.

 

“Let him in,” Elizabeth says, and Rodney lowers the shield.

 

Sheppard steps through the gate, followed by a rush of _people_ , most of whom are decidedly _not_ Marines.

 

-x-

 _SHIELD FAILURE IMMINENT_ flashes across the screen, and Rodney _knows_ he’s starting to panic now, but he can’t _help_ it. “The shield is collapsing!”

 

A light washes over the city as the shield begins to fail entirely, followed by a deep rumbling as the base suddenly jolts so hard that everyone falls off their feet. The vertigo that results is reminiscent of a roller coaster, or a particularly fast elevator, a swoop in the bottom of Rodney’s stomach like a lead weight suddenly in his throat. (He knows the words for this, of gravitational force and acceleration and free-fall, and all the other little things that make it up, but in the moment, all he knows is _fear_.)

 

Boxes and crates (and _people_ ) fall and crash and smash against each other, other people scrambling to find something _sturdy_ to keep them as upright as possible.

 

“I’m dialing an address,” Grodin says.

 

Before Rodney can manage a response, Elizabeth yells, “No, wait!”

 

“She's right,” Rodney supports, because she is. There was no sudden rush of water and crash of flood.

 

Because they’re not _drowning_ \--the city is _rising_ instead.

 

“We're moving!” Sheppard yells, and it was obvious to Rodney but the sudden relief on most of the rest of the faces tells him that it hadn’t been obvious to them. ( _Proof_ , a part of him supplies, _that they’re not as smart as he is._ )

 

As the city breaks the surface, the bright alien sunlight starts to filter through the windows of the Control Room. Once it settles, the internal lights flicker back on. It doesn’t take long for most of them to rush to the closest windows, watching as the water cascades down the windows and off spires and piers and metal.

 

“We’re on the surface,” one of the Marines says in awe.

 

“I was hoping for another day,” Elizabeth says, that odd tone back in her voice, “Looks like we just got a whole lot more than that. Let's not waste it.”

 

-x-

 

It's stupid, Rodney thinks, because he hasn't actually known John Sheppard all that long.

 

But somehow in between nights in Antarctica, dancing back and forth between the Chair and his lab, and then in the Mountain, under miles of concrete and steel in his temporary lab, he thinks that maybe he's gained a friend.

 

He’s known since he was young and afraid that he didn't actually make friends all that easily. That there was something _wrong_ in him that pushed people away before he ever really got to know them, and over the years, he did the pushing actively with abrasive words and a cutting tongue.

 

Everyone who had been in the Mountain before the absolute debacle that sent him to Siberia had never truly given him a chance because of who he was, in the end. They worshipped Samantha Carter, and most days he thought it was rightfully so. She was beautiful and smart and she knew it.

 

He’d wanted her, of course. There was just something about her that drew him in, and he didn't think it was the breasts. Or perhaps, more accurately, _just_ the breasts.

 

But he didn't think he ever really stood a chance, even before the thing with Teal’C. It didn't help that he was the way he was, that he came on too strong and was too much of an “unfeeling asshole”. Which, he was okay with the asshole part. It was accurate.

 

But unfeeling had never been a part of it. He wasn't a sociopath or a psychopath, whatever the voodoo terminology was. He just, he had learned when he was young that showing emotion was worse than feeling it. He’d learned over his brief time active with the CIA, that no matter what his personal feelings about it were, the many were more important than the few 90% of the time.

 

He felt, he had always felt. He couldn't have raised Jeannie otherwise.

 

But showing people his _feelings_ wasn't something he was capable of doing that easily anymore. He wasn't really sure who sparked that lesson the most--his parents, his ex-wife, his handler, his colleagues or, if he was honest, his sister. But it was a lesson he'd learned nonetheless.

 

“It's easier to hide in plain sight,” someone had told him once. And it was true. Rodney stopped lying about it and started telling the brutally honest truth--even when that truth was more opinion that determinable fact.

 

He’s not used to having friends. Not used to having someone he can actively rely on, because that's a lesson he'd learned over the years too.

 

But Carson had somewhat become his friend before Sheppard had set one foot in the base, or at least someone who didn't actively hate him.

 

And for awhile, he thought Elizabeth was. Though, and he wouldn't share the information with anyone else, she seemed to be cracking under the pressure and he wasn't sure he liked the woman she was proving to be.

 

But John Sheppard, he stepped into his life one day and shook everything up just by existing. He looked at Rodney with wide surprised eyes, leaning back in the Chair for a second, just a second, Rodney thought that maybe this was what love at first sight was supposed to be.

 

And then he told Sheppard to picture the solar system and there it was and he felt that same wild appreciation for the hologram above him.

 

He didn't expect to see much of Sheppard after that. He'd been there while Elizabeth and Sumner fought like cats and dogs over his inclusion in the expedition, and he thought that ultimately Sumner would win.

 

But then, Sheppard walked into his lab not even a week later, looking a little tired but that smirky little smile still plastered on his face.

 

Rodney had done what he always did when faced with the things he desperately wanted but didn't deserve. He ranted and raved and verbally eviscerated.

 

But instead of upset or angry, Sheppard looked amused. And sometimes, he even bit back with sarcasm and a quip.

 

In the months that follow, Rodney isn't quite as afraid anymore, of Sheppard wandering off to play verbal tennis with one of the other scientists.

 

Sheppard keeps coming back to his lab, after all. Even late at night when pretty Majors should be asleep.

 

He doesn't expect the kiss, chaste as it is. He doesn't remotely expect it.

 

He’d been trolled before--viciously in fact--by people who pretended to like him just to prank him. To throw his attitude and ego in his face like last night’s trash.

 

But John came to his lab night after night without doing anything to suggest he wanted to kiss him or kill him, seemed amused when he reamed out his subordinates, and mostly unoffended when he was insulted.

 

He doesn't know why John kissed him, when they were alone with a deadline looming over their heads, just to leave before he can formulate any kind of response.

 

He wants to know, desperately wants to know. And there's a part of him--a very big part of him, whether he admits it or not--that wants John to say it's because he _likes_ him, pure and simple.

 

He isn't thinking about the kiss or the potential disaster behind it when he corners Sheppard after discovering the reality of the space gate.

 

He's just thinking, Sheppard is someone who doesn't leave people behind. There's a black mark in his file that proves it.

 

And the ships, in the hanger. They could make sure he doesn't have to.

 

-x-

 

So he brings hope to him by walking him to the hanger, into one of the ships. And watches.

 

Rodney _watches_ as John touches the control panel in front of him just barely, color flaring up under his fingertips.

 

“Think you can fly it?” He asks, and the grin Sheppard gives him is almost blinding.

 

“What do you say we find out?” Sheppard asks, sitting down in the pilot seat like he belongs there.

 

And maybe he does--he looks like he fits there, in a way that Rodney can't find the words for.

 

“Yeah,” Rodney manages, fully aware at how rough his voice sounds, “We should do that.”

 

Sheppard looks away from the ship then, his eyes _searching_ him in a way that should feel intrusive but somehow isn't.

 

“About before,” Sheppard starts, and Rodney shakes his head.

 

“We don't have to--”

 

“No, I did what I wanted to do. I just... wanted you to know that.”

 

“What? You just wanted to kiss me so you could say you--”

 

John’s out of the pilot’s chair and pressing his mouth to Rodney’s before Rodney can even manage to say another syllable.

 

His mouth is warm and wet and tastes like weak coffee and something indecipherable but wholly John. Rodney doesn't really think about _how_ to respond, just _does_ it, presses into him and kisses back just as fiercely, just as much.

 

John--because it sure as hell isn’t Sheppard now--pulls back a minute later and looks at Rodney for a long drawn out moment, then closes his eyes and takes a deep breath.

 

“I wanted to kiss you because I like you,” he whispers, “and I still do.”

 

“... Why?” The question slips out of his mouth before he can stop it. Because he doesn't _get it_.

 

“You're like [the Euler-Lagrange equation](http://www.bbc.com/earth/story/20160120-the-most-beautiful-equation-is-the-euler-lagrange-equation),” John says, and something about the tone of his voice makes his stomach squirm in that flattered ecstatic way.

 

“Like--you know _Euler-Lagrange_?”

 

“It looks simple, you know? But it's so much more than that. It's...”

 

And Rodney kisses him then, he has to. He _wants_ to.

 

Because John shared something about himself that meant something to him, something that had weight in how he viewed the world, in how he viewed _Rodney_.

 

And it was _math._

 

It was almost like looking through a viewfinder and only seeing every other panel and then suddenly being able to see the whole scene. You could create a story without it, but it wouldn't be the same picture as the one that was real.

 

So he kisses John, gives in to all the emotion and want and need in him.

 

And when John pulls back, he's smiling.

 

-x-

 

It's oddly difficult, afterward, to watch John leave without him. As if that's something he's used to, going Offworld at John’s side. Almost as if the whole idea of them being in danger and separated is contemptuous and wrong.

 

Every other relationship that Rodney had ever been in, distance was easy. Sometimes he preferred it that way.

 

Maybe it shouldn't have come at such a surprise to him, that he would want to be at John’s side here.

 

Maybe.

 

Elizabeth says loudly as the ship is about to go through the gate, “Be safe.”

 

And Rodney repeats it, under his breath in a whisper, “be safe.”

 

-x-

 

For a few minutes, while they continue to wait to hear from Sheppard, Rodney escapes into the hangar. It's quiet, empty, still.

 

He doesn't feel like everyone’s emotions are tangling up underneath his skin here, like everyone’s projecting their spiking worry and fear directly into his head.

 

He tries to breath and it comes out shuddering and stuttered. Rodney knows he's about to hyperventilate, but he doesn't know how to stop it. For _hours_ he had every person’s hope pinned on him, and other than the moment with John, in the ship, he had no reprieve to let himself settle. There hadn't been any moment where the reality of what was happening was allowed to fully hit him, just the highlights of tension and panic of everyone else to spurn his need to save them and thus override his natural state of uncontrolled fear.

 

And now, for a moment, he was alone.

 

The person he cared most about, in this galaxy, was off risking his life without him, and somehow, inexplicably, he thinks that hurts more than anyone in his past had ever made him hurt.

 

He starts hyperventilating, his hands shaking as he fists one in his shirt as if to help himself breathe and the other brushing back the wetness from his face.

 

Something brushes against his leg then, something small and warm and familiar.

 

He thinks, for a blissful calming moment, that he sees a purring cat brushing up against him.

 

But then the image and the feeling are gone.

 

And so is his panic.

 

-x-

 

“Take the shot, Major,” Sumner barely moves his lips to stutter the words, and somehow they sound like screams in his head.

 

He shoots, his hands unsteady against his will. It’s a good shot, straight through the thing’s head. There’s a splash of dark blood on Sumner’s face, but the bullet mostly misses _his_ head.

 

But the thing is still attached to his chest, and John knows he has to do _something_.

 

“I won’t tell you,” Sumner gasps as his face grows older still.

 

And John shoots again, once, twice, three times. Four.

 

Bates matches him with every shot, still as wild-eyed as he’d been when John found him.

 

The thing, _female_ , screams loud and strong and long.

 

But then it--she--falls backward, and starts to laugh. Dark, disturbing giggles that make him shudder.

 

The hand stays where it had been, attached to Sumner’s chest. Sumner collapses backward, splattered in blood, and John can’t tell if he’s alive.

 

“You don't know what you have done. We are merely the caretakers for those that sleep. When I die, the others will awake,” she laughs, and the rush of blood that gurgles out of her mouth does little to stop her speech, “ _All of them_.”

 

“We have to go,” Ford says over the radio, and Bates nods when Sheppard reiterates it.

 

Neither of them immediately turn to leave though.

 

Even if Sumner is already dead, he doesn't deserve to be left here.


	3. Part Three

**Notes for the Chapter:**

> Huge thanks to popkin16 for her input, even though I gave her only the vaguest knowledge of what I was asking.
> 
> I'm going to be honest. MOST of this was written weeks ago, but I had a lot of thinking to do about where I was headed. I know what's happening now, Nanowrimo is over, and it's time to continue. :)
> 
> There is also an updated chapter count. This particular story was never going to be HUGE. But it will have a sequel, as their journey is far from over. In the mean time, I hope you enjoy. <3

“Take the shot, Major,” Marshall whispers, the words too low for the creature in front of him to hear, agony rippling through his bones like blood flows in his veins.

 

The bullet pierces right through the thing’s forehead, ricocheting out and shearing the side of his head. It hurts, but nothing hurts as badly as the thing in front of him, turning him into a shrunken cask of a human, tearing secrets out of his head like a child picking candy from a bowl.

 

“I won't tell you,” he rasps, his voice growing weaker as his body loses the sufficiency to be.

 

The last thing he sees before everything goes out is a hail of bullets ripping through the creature. The last thing he hears is its scream.

 

_Good_.

 

-x-

 

John is tired. He is tired, exhaustion seeping into every part of him like a stain. He is tired and wrung out and sluggish, but he can’t let it show.

 

He’s in charge now, by default. Even if Sumner survives, something that doesn’t seem likely given what he looked like when they carried his body to the Puddlejumper, he won’t be able to lead the way he is.

 

He’s in charge of a _battalion_ of Marines who have no connection with him, no reason to respect him given his record.

 

He doesn’t want this, any of it.

 

He just wants the City and Rodney and flying and math.

 

“Major Sheppard?” Elizabeth Weir asks, and he pastes a smile across his lips and turns to face her.

 

“Yes, Dr. Weir?” he asks, and doesn’t flinch when she touches his arm with her hand.

 

“Elizabeth, please,” she says, and she’s still holding his arm, “I understand you're taking over for Colonel Sumner?”

 

“Looks that way.”

 

“...Major Sheppard,” Rodney says--he would know that voice anywhere--but it takes John a moment to find him across the room. _Across the room?_

 

He steps forward, out of Elizabeth’s grasp, and he knows she’s saying something but the words aren’t really registering.

 

Is that Rodney’s _heartbeat?_

 

-x-

 

“--bite your tongue off, Major--”

 

“--he’s having a zone-out, Rodney, not a seizure--”

 

A zone-out?

 

He’s... _online?_

 

-x-

 

“I’m _fine_ , Doctor Beckett,” Sergeant Bates is saying when John finally comes to. His voice is louder than it should be.

 

“You and the Major came online in the middle of battle, Sergeant,” Beckett says, “I cann--”

 

“Loud,” John manages to say, and he doesn’t like the way his words slur in his mouth.

 

“Major Sheppard?” Beckett asks, leaning over him. It almost sounds like a scream, but John knows that can’t be right. Beckett’s mouth is hardly moving.

 

“Doctor,” John manages, and the room suddenly goes dark.

 

“Rodney--” Beckett says, sounding annoyed.

 

“Yes, well he’s obviously having trouble regulating his senses after violently coming online during our _Hurray, We’re Alive_ party, so forgive me for thinking he might want one less thing to focus on.”

 

“McKay?” John asks, as some of the auxiliary lights flicker back on.

 

“Why is he slurring? Major--”

 

“He had an atypical reaction to the sedative, Rodney. He’ll be fine in a few hours.”

 

That was good to know, why hadn’t Beckett told him that?

 

“Loud,” John repeats, because Beckett still _was_ loud.

 

“Ah, yes, Major,” Beckett says, and he’s pretty sure Beckett’s whispering to him now, even though it’s still loud.

 

-x-

 

When John was fifteen, he spent a week at a camp for latent sentinels. It wasn’t much different from a regular camp, except that they spent two hours every morning going over the basic practices of being an active sentinel.

 

Dials and switches and zippers, focuses and guides.

 

The thing is, John remembers all of that, but ultimately that’s not what works for him.

 

-x-

 

He thinks of exponential functions, of growth and decay. He thinks of the curve drawn out on a graph, and where his senses lie.

 

It’s not _easy_ , but it works, somehow.

 

But that doesn’t surprise him, not really.

 

No matter how hard he’s tried, he never fit the model of what he was _supposed_ to be.

 

-x-

 

“You’ll need to find a guide,” Beckett admits, finally signing his release. John shrugs. He knows that Beckett is right. He’s already zoned out twice since Beckett had been forced to sedate him last night, and the quick tests to measure his senses rank him far higher than either of them had expected.

 

“We’re separated from Earth,” John reminds him, and Beckett sighs.

 

“Bonding with someone here would be the best, but a temporary guide should at least help settle you.”

 

-x-

 

“Major Sheppard,” one of the scientist says, knocking on the door frame of John’s open bedroom.

 

“Yes?” John responds, sitting up and putting his book on the mattress beside him.

 

“I'm Dr. Parrish,” the man says, hesitantly, “Dr. Beckett sent me.”

 

John sighs, because he isn’t surprised.

 

“You’re not my guide,” John says, and the other man relaxes with a sigh.

 

John raises an eyebrow at the reaction, and Parrish flushes.

 

“It’s not you,” Parrish says, and John thinks he means it, “I just want to get used to everything here before I commit like that.”

 

-x-

 

The thing is, John knows that not everyone subscribes to the belief that there’s a Guide for every Sentinel, one specific person in all the world that they’re meant to be paired with. But John had hung onto that belief his entire life. He liked the idea, that no matter what happened, no matter what he did or didn’t do, whether he ever came online or not, there was _someone_ out there who was meant for him.

 

Dr. Beckett tells him that he needs a guide in the here and now, someone to steady him. They’ve already seen firsthand that this galaxy is dangerous, far too dangerous for the de facto military leader to remain untethered. And John knows he’s right.

 

But John doesn’t want a _Guide_ ; he wants _Rodney_.

 

John knows his guide isn’t one of the handful of online personnel with them in Atlantis. He doesn’t know _how_ he knows it, but he knows that the three men and two women who Beckett sends his way aren’t _his_.

 

John wishes, fervently, that Rodney was a guide. That Rodney was _his_ Guide. That he didn’t have to pick someone to have at his side who wasn’t Rodney.

 

But Beckett says, “we have five online unbonded guides on record,” and “there are six latent, of course,” and “you need _someone_.”

 

Beckett isn’t telling John anything he doesn’t already know.

 

John doesn’t want his fated Guide, not anymore. He wants Rodney, and now the universe seems to be telling him he won’t be able to keep him.

 

-x-

 

“Rodney,” John hears, waking up suddenly from what had been his first truly restful sleep since he arrived.

 

“So much,” and that’s _Rodney’s_ voice he’s hearing, “so much, so much, it hurts.”

 

John’s room is _empty_ , but he can still hear Rodney screaming.

 

-x-

 

He follows the sound of Rodney’s voice through the corridors and halls of Atlantis, rushes past the marine on patrol without a word. By the time he reaches the infirmary, he has two marines behind him and Weir’s voice screeching in his ear through his radio.

 

He ignores them, nothing but the _need_ to get to Rodney in his mind.

 

“Major Sheppard--” a nurse tries to stop him, a hand outstretched in his direction. He bats it away, searching for Rodney’s face.

 

John rips the radio out of his ear when it turns into a cacophony of sound, his tense shoulders only relaxing when he finally sees Rodney.

 

“ _Rodney_ ,” John hears it come out of his own mouth, a strangled noise barely decipherable as a word let alone a name but John knows what it is anyway.

 

“Major, what are you--” Beckett says, surprised by John’s sudden appearance at Rodney’s bed. Rodney is sitting in the middle of an infirmary cot, both hands pressing into his head. He reminds John of a petrified child, rocking himself as he covers his ears. Except, Rodney isn’t covering his _ears_.

 

Nothing about Rodney at first look would scream latent Guide, and as far as John knows Beckett would know if Rodney had been. Except everything John can see _now_ tells him that Rodney is in a full-blown _Guide_ awakening.

 

The infirmary is suddenly cast into darkness, the lights going out without a sound. The steady beat of the machinery in the isolation room nearby keeps going despite the sudden power loss, but John doesn’t let himself think about why.

 

The door chimes, the marines at his side and the nurse and _Beckett_ all clamoring around confused and likely afraid.

 

Rodney screams, a guttural thing that John feels down to his bones.

 

“Back away,” John growls, pushing Beckett none too gently away from Rodney.

 

“He’s in pa--” Beckett starts, but John doesn’t care why Beckett hasn’t noticed.

 

“He’s _online_ ,” John says, grasping one of Rodney’s arms.

 

“McKay’s not a Sentinel,” the nurse says snottily, her arms crossed over her chest.

 

“That’s because he’s a _Guide_ ,” Sergeant Bates says from the doorway, flanked on either side by the expedition’s bonded Sentinel-Guide pair.

 

The guide--Stackhouse, if John’s memory serves correct--swans into the room without waiting for an invitation, very carefully slipping past John to Rodney’s side.

 

John barely has enough thought to stifle a _growl_ from the back of his throat before a sudden faint feeling of calm washes over him.

 

“We need to get McKay out of here. Colonel Sumner’s pain alone is deafening and my shields are up,” Stackhouse tells them, and John doesn’t hesitate to join Stackhouse in helping Rodney to stand.

 

Stackhouse exudes calmness, enough that John doesn’t remember the last time he felt so serene. It’s false--John has spent too many years in warzones to think he could ever really feel this way again--but it’s not _bad._

 

Between him and Stackhouse, they manage to lead Rodney out of the infirmary and in the direction of the housing they’d set up. Bates walks just ahead of them, Stackhouse’s sentinel Markham behind them.

 

When they reach Rodney’s quarters, there are a number of scientists and military personnel alike standing guard. All of them are online Sentinels and Guides that Beckett had informed John about, every single one.

 

John feels an overwhelming sense of _family_ , surrounded by these people. They’re mostly strangers, except for Rodney. But yet...

There’s a Sentinel prerogative that John has heard about, learned about. The need to form familial bonds between the people under their wing, to form a _tribe_ between them.

 

The years wore John down off the belief that he would ever lead one, let alone be _part_ of one. Somehow, he thinks he should be less surprised that he seems to be doing exactly that without even trying.

 

-x-

 

They settle Rodney into bed easily enough, the over-exhausted scientist finally relaxing once he’s in his own bed. John doesn’t know what he’s supposed to do now, if he’s supposed to do anything at all.

 

Stackhouse lets out a long, deep sigh and stands back up wearily.

 

“My Sentinel and I will be in the room next door. We’ll set up guards between the rest of us while McKay gets some rest. He’s... the two of you are going to be something really special, you know?” Stackhouse says, and John can’t help but believe he means it.

 

“Thank you,” John says, not as surprised as he should be when it comes out softly.

 

“Anytime, Sentinel Sheppard,” Stackhouse replies, emphasizing his title.

 

John slumps down onto the floor when Stackhouse leaves, leans his back against Rodney’s bed. He falls asleep like that, the sound of Rodney’s even breathing and steady heartbeat like a lullaby.

 

-x-

 

When John had asked Nancy to marry him, he had believed that he could make it work. That he would be a good husband, a good lover, a good friend.

 

In the end, he’d only ever been a good airman.

 

-x-

 

The thing is, when John wakes up in the early morning, the noise of Rodney waking like a strange alarm clock, he isn't thinking about Nancy and how he’d been sure he could make it work. He isn't thinking about how much easier just being around Rodney is. He's just, for the brief few moments they're alone together in the soft light of morning, content to be.

 

-x-

 

“I'm a _Guide?”_ Rodney asks him once he's awake enough to process.

 

“You came online strongly enough that all the Sentinels and Guides on base felt it,” John admits, watching Rodney carefully.

 

“I... How can _I_ be _anyone’s_ Guide?” Rodney asks, and John doesn't like the way those words feel.

 

“You're not just anyone’s Guide, McKay,” John says, grasping Rodney’s arm to pull him closer.

 

“What--”

 

“Rod _ney_ ,” John stresses, and Rodney almost _softens_.

 

“You really believe that? It's not just... guide pheromones?”

 

“Guide phero--did everything you know about Sentinels and Guides come from _porn?”_

 

“N-no,” Rodney says and John doesn't miss the stutter of his heartbeat over the lie.

 

“Don’t ever change, Rodney,” John says, and kisses him.

 

It isn't any different than the rest of their kisses but it’s also somehow _more_. It's like there's an echo of the feeling in his head, like _coming home_ and _happiness_.

 

And maybe that's Rodney, instinctively sending his feelings about it to John as it happens. Or maybe it's the fledgling bond itself, recognizing _online_ and _aware_ and _intent._

 

He doesn't know. He doesn't care. As long as he gets to keep this, he's not sure anything else matters.

 

And then the door slides open with a sickening crack that almost hurts his _teeth._

 

“Apologies,” the man at the controls outside the door says, waving his hand in their direction, “We were unable to reach either of you.”

 

Dr. Weir makes no such apology, stepping into Rodney’s room without asking.

 

“This is a serious violation of pol--”

 

“You need to leave,” Rodney says, his hand tightening on John’s hip.

 

“...  excuse me? Dr. McKay--”

 

“Dr. Weir, I believe my guide asked you to leave.”

 

“I can't believe this, Dr. McKay, you are to be stripped of your position as head of the science department and your second in command--”

 

“You cannot do that, Doctor Weir,” the man at the door protests, both hands free of the door.

 

“Radek--”

 

“It is Dr. Zelenka to you, ma’am. And you cannot strip McKay of his position because he is, how to phrase, fraternizing with the military commander. For one, I do not wish to take over. But also, Dr. McKay is the Chief Guide of the expedition. You have no authority over his relationship with the Chief Sentinel, nor have any recourse should you be against it. It is sacred.”

 

_Radek Zelenka_. John commits the name to memory. He’s one of the few non-military Sentinels on base, and one that he had no true prior personal experience with. And Rodney had never called him the correct name before.

 

“You’re sick,” Rodney blurts out, his eyes wide as he stares at Weir.

 

“That--you can't _say that_.”

 

“It's true,” Stackhouse says from the doorway, flanked by Bates and Markham in full dress.

 

“I'm not ill,” Weir protests.

 

“Not physically,” Rodney says, and John can feel Rodney’s uneasiness.

 

“There isn't anything--”

 

“You're not latent,” Stackhouse suddenly interrupts, his voice oddly pitched.

 

“Of course I am! I've been waiting to come--”

 

“You're _dormant_.”

 

-x-

 

Dormant.  _Dormant_.

 

Rodney has never felt something so _wrong_ before. It’s like he can suddenly put a name to the slowly growing discomfort he had in regards to Elizabeth.

 

It feels like a discordant sound, a hollowness inside his chest that makes him want to throw up.

 

“Take her to Carson,” Rodney chokes out, her sickness pervading further and deeper into his head the longer she’s near him.

 

“Right away, Guide McKay,” Sergeant Bites says with a tone of respect, and it occurs to Rodney for the first time that he’ll have to remember his name now. 

 

 

**Author's Note:**

> I am really loving this fic so far, so your comments, questions, and concerns are _very_ welcome. :)  
>  You can find me on tumblr as [writerdragonfly.](http)


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